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(-) Description

Title :  CRYSTAL STRUCTURE OF METHIONYL-TRNA FORMYLTRANSFERASE FROM YERSINIA PESTIS COMPLEXED WITH L-METHIONINE
 
Authors :  N. Maltseva, Y. Kim, J. Hasseman, W. F. Anderson, A. Joachimiak, Center Structural Genomics Of Infectious Diseases (Csgid)
Date :  24 Mar 11  (Deposition) - 13 Apr 11  (Release) - 13 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.26
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Alpha Beta Structure, Formyltransferase, Cytosol, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Maltseva, Y. Kim, J. Hasseman, W. F. Anderson, A. Joachimiak, Center For Structural Genomics Of Infectious Diseases (Csgid)
Crystal Structure Of Methionyl-Trna Formyltransferase From Yersinia Pestis Complexed With L-Methionine
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - METHIONYL-TRNA FORMYLTRANSFERASE
    Chains: A
    EC Number: 2.1.2.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21MAGIC
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: FMT, Y4022, YPO0241, YP_0239
    Organism Scientific: YERSINIA PESTIS
    Organism Taxid: 632
    Strain: CO92

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric Unit (4, 6)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2MET1Mod. Amino AcidMETHIONINE
3MOE1Ligand/IonMETHOXY-ETHOXYL
4TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (4, 6)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2MET1Mod. Amino AcidMETHIONINE
3MOE1Ligand/IonMETHOXY-ETHOXYL
4TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 2 (4, 12)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL
2MET2Mod. Amino AcidMETHIONINE
3MOE2Ligand/IonMETHOXY-ETHOXYL
4TRS2Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:90 , TYR A:91 , GLY A:92 , ASN A:109 , HIS A:111 , GLY A:120 , ASP A:147 , GOL A:324 , HOH A:353BINDING SITE FOR RESIDUE MET A 320
2AC2SOFTWAREALA A:101 , MET A:102 , ARG A:104 , GLU A:162 , GLN A:250 , ALA A:251 , THR A:285 , MOE A:323 , HOH A:326 , HOH A:328BINDING SITE FOR RESIDUE TRS A 321
3AC3SOFTWAREGLU A:72 , GLU A:199 , THR A:200 , ALA A:202 , ASP A:299BINDING SITE FOR RESIDUE GOL A 322
4AC4SOFTWAREGLU A:162 , ILE A:228 , ARG A:229 , TRP A:249 , GLN A:250 , TRS A:321 , HOH A:328BINDING SITE FOR RESIDUE MOE A 323
5AC5SOFTWAREPHE A:15 , ALA A:90 , GLY A:112 , PRO A:123 , MET A:320 , HOH A:349 , HOH A:392BINDING SITE FOR RESIDUE GOL A 324
6AC6SOFTWAREPRO A:255 , GLN A:274 , HOH A:370 , HOH A:418BINDING SITE FOR RESIDUE GOL A 325

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3R8X)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Leu A:115 -Pro A:116
2Asn A:232 -Pro A:233
3Trp A:234 -Pro A:235

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3R8X)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GARTPS00373 Phosphoribosylglycinamide formyltransferase active site.FMT_YERPE136-159  1A:136-159
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GARTPS00373 Phosphoribosylglycinamide formyltransferase active site.FMT_YERPE136-159  1A:136-159
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GARTPS00373 Phosphoribosylglycinamide formyltransferase active site.FMT_YERPE136-159  2A:136-159

(-) Exons   (0, 0)

(no "Exon" information available for 3R8X)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:310
 aligned with FMT_YERPE | Q8ZJ80 from UniProtKB/Swiss-Prot  Length:315

    Alignment length:317
                             1                                                                                                                                                                                                                                                                                                                       315 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309     | 
            FMT_YERPE     - -MSDSLRIIFAGTPDFAARHLGALLSSQHKIVGVFTQPDRPAGRGNKLTPSPVKILAEHHGIPVFQPKSLRPEENQHLVADLNADIMVVVAYGLILPAAVLAMPRLGCINVHGSLLPRWRGAAPIQRSVWAGDEKTGITIMQMDIGLDTGAMLHKIECAIQPEDTSATLYDKLAQLGPQGLLITLQQLAAGTALAEVQNETQATYAEKLSKEEAKLDWTLSATQLERCIRAFNPWPVSYFIVDEQPIKVWQAQVLPAGEDAEPGTIIHADKHGIQVATADGVLNITQLQPAGKKAMSAADLLNSRREWFIPGSQLV-   -
               SCOP domains d3r8xa1 A:0-207 automated matches                                                                                                                                                                               d3r8xa2 A:208-314 automated matches                                                                         - SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----Formyl_trans_N-3r8xA02 A:5-184                                                                                                                                                      ----------------------Formyl_trans_C-3r8xA01 A:207-305                                                                   --------- - Pfam domains
         Sec.struct. author ......eeeeee.hhhhhhhhhhhhhh..eeeeee......------...hhhhhhhhhh...ee..........hhhhhhh...eeeee......hhhhhh.....eeeee.......ee.hhhhhhhhh...eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhh.ee..............hhhhhhhhhhhh......eeee..eeeeeeeeeee..........eeeee..eeeee....eeeeeeeee.....eehhhhhhhhhhhhh.....-. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------GART  PDB: A:136-159    ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r8x A   0 AMSDSLRIIFAGTPDFAARHLGALLSSQHKIVGVFTQPDRP------LTPSPVKILAEHHGIPVFQPKSLRPEENQHLVADLNADIMVVVAYGLILPAAVLAMPRLGCINVHGSLLPRWRGAAPIQRSVWAGDEKTGITIMQMDIGLDTGAMLHKIECAIQPEDTSATLYDKLAQLGPQGLLITLQQLAAGTALAEVQNETQATYAEKLSKEEAKLDWTLSATQLERCIRAFNPWPVSYFIVDEQPIKVWQAQVLPAGEDAEPGTIIHADKHGIQVATADGVLNITQLQPAGKKAMSAADLLNSRREWFIPGSQL-M 320
                                     9        19        29        39|      |49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309    | |
                                                                   40     47                                                                                                                                                                                                                                                                        314 |
                                                                                                                                                                                                                                                                                                                                                      320
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3R8X)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Formyl_trans_C] (5)
(-)
Clan: no clan defined [family: Formyl_trans_N] (25)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (FMT_YERPE | Q8ZJ80)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016742    hydroxymethyl-, formyl- and related transferase activity    Catalysis of the transfer of a hydroxymethyl- or formyl group from one compound (donor) to another (acceptor).
    GO:0004479    methionyl-tRNA formyltransferase activity    Catalysis of the reaction: 10-formyltetrahydrofolate + L-methionyl-tRNA + H2O = tetrahydrofolate + N-formylmethionyl-tRNA.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    GO:0071951    conversion of methionyl-tRNA to N-formyl-methionyl-tRNA    The modification process that results in the conversion of methionine charged on a tRNA(fMet) to N-formyl-methionine-tRNA(fMet).
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
    GO:0006413    translational initiation    The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA.

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